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PhaseByTransmission

Compute the most likely genotype combination and phasing for trios and parent/child pairs

Category Variant Discovery Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

This tool performs two functions:

  1. Compute the most likely genotype combination of trios and parent/child pairs given their genotype likelihoods and a mutation prior;
  2. Phase all sites were parent/child transmission can be inferred unambiguously.

The tool ultimately reports the genotype combination (and hence phasing) probability.

Ambiguous sites are:

  • Sites where all individuals are heterozygous
  • Sites where there is a Mendelian violation

Missing genotypes are handled as follows:

  • In parent/child pairs: If an individual genotype is missing at one site, the other one is phased if it is homozygous. No phasing probability is emitted.
  • In trios: If the child is missing, parents are treated as separate individuals and phased if homozygous. No phasing probability is emitted.
  • In trios: If one of the parents is missing, it is handled like a parent/child pair. Phasing is done unless both the parent and child are heterozygous and a phasing probability is emitted.
  • In trios: If two individuals are missing, the remaining individual is phased if it is homozygous. No phasing probability is emitted.

Input

  • A VCF variant set containing trio(s) and/or parent/child pair(s).
  • A PED pedigree file containing the description of the individuals relationships.

Important options

  • MendelianViolationsFile: An optional argument for reporting. If a file is specified, all sites that remain in mendelian violation after being assigned the most likely genotype combination will be reported there. Information reported: chromosome, position, filter, allele count in VCF, family, transmission probability, and each individual genotype, depth, allelic depth and likelihoods.
  • DeNovoPrior: Prior probability of de novo mutations. The default value of 1e-8 is fairly stringent, so if you are interested in maximizing sensitivity at the expense of specificity (i.e. are ok with seeing some false positives as long as all true positives are detected) you will need to relax this value.

Output

An VCF with genotypes recalibrated as most likely under the familial constraint and phased by descent (where non ambiguous).

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T PhaseByTransmission \
   -R reference.fasta \
   -V input.vcf \
   -ped input.ped \
   -o output.vcf
 

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by PhaseByTransmission.


Command-line Arguments

Engine arguments

All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.

PhaseByTransmission specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Inputs
--variant
 -V
NA Input VCF file
Optional Outputs
--out
 -o
stdout An output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--DeNovoPrior
 -prior
1.0E-8 Prior for de novo mutations. Default: 1e-8
--MendelianViolationsFile
 -mvf
NA File to output the mendelian violation details.
Optional Flags
--FatherAlleleFirst
 -fatherAlleleFirst
false Ouputs the father allele as the first allele in phased child genotype. i.e. father|mother rather than mother|father.

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.


--DeNovoPrior / -prior

Prior for de novo mutations. Default: 1e-8

double  1.0E-8  [ [ -∞  ∞ ] ]


--FatherAlleleFirst / -fatherAlleleFirst

Ouputs the father allele as the first allele in phased child genotype. i.e. father|mother rather than mother|father.

boolean  false


--MendelianViolationsFile / -mvf

File to output the mendelian violation details.

PrintStream  NA


--out / -o

An output file created by the walker. Will overwrite contents if file exists

VariantContextWriter  stdout


--variant / -V

Input VCF file
Variants from this VCF file are used by this tool as input. The file must at least contain the standard VCF header lines, but can be empty (i.e., no variants are contained in the file).

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3

R RodBinding[VariantContext]  NA


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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.